iqtree
TLDR
Run phylogenetic analysis
$ iqtree -s [alignment.fasta]
Specify model$ iqtree -s [alignment.fasta] -m [GTR+G]
Automatic model selection$ iqtree -s [alignment.fasta] -m MFP
Bootstrap analysis$ iqtree -s [alignment.fasta] -b [1000]
Ultra-fast bootstrap$ iqtree -s [alignment.fasta] -bb [1000]
Use multiple threads$ iqtree -s [alignment.fasta] -nt [4]
SYNOPSIS
iqtree [options] -s alignment
DESCRIPTION
IQ-TREE is a phylogenetic analysis tool for maximum likelihood tree inference. It supports various substitution models, model selection, and multiple bootstrap methods.
IQ-TREE is known for its speed and accuracy, implementing efficient algorithms for large-scale phylogenetic analysis. It handles DNA, protein, codon, and morphological data.
PARAMETERS
-s file
Input alignment file.-m model
Substitution model (or MFP for selection).-b n
Standard bootstrap replicates.-bb n
Ultra-fast bootstrap replicates.-nt n
Number of CPU threads.-pre prefix
Output file prefix.-o taxa
Outgroup taxa.-t tree
Starting tree file.-wbt
Write bootstrap trees.-alrt n
SH-like approximate likelihood ratio test.
OUTPUT FILES
$ .treefile Best tree in Newick format
.iqtree Analysis report
.log Screen log
.mldist ML distances
.bionj BIONJ starting tree
.iqtree Analysis report
.log Screen log
.mldist ML distances
.bionj BIONJ starting tree
CAVEATS
Large alignments require significant memory. Model selection can be time-consuming. Bootstrap numbers vary by study requirements.
HISTORY
IQ-TREE was developed by Bui Quang Minh, Lam-Tung Nguyen, and Arndt von Haeseler at the University of Vienna. First released in 2014, it's become a standard tool for molecular phylogenetics.
